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Skills

R
Python
Bash

Languages

Russian
English
German

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The source code is available on github.com/nstrayer/cv. Modified source code for this CV is available here

Last updated on 2023-09-11.

Main

Evgeniia Chikina

I am a bioinformatician with a medical background. I use my medical and biological knowledge to combine with the world of computer science. At the moment, I have particularly good knowledge and skills in analyzing single cell RNA sequencing data.

Education

PhD Student, Cellular biology

Koltzov Institute of Developmental Biology of Russian Academy of Sciences

Moscow, Russia

Current - 2022

Master’s degree (with honors), Applied Mathematics and Informatics, Bioinformatics and System Biology

ITMO University

Saint-Petersburg, Russia

2022 - 2020

  • Thesis: Metabolic Modules Identification in Single-Cell Data
  • Course Project: Identifying Metabolic Modules in TCGA Datasets
  • Semester Project: Effects of Background RNA Noise on Differential Expression Results in scRNA-seq

Specialist degree (with honors), Pediatrician

Saint-Petersburg State Pediatric Medical University

Saint-Petersburg, Russia

2020 - 2014

  • Pediatrician

Research Projects

Metabolic Modules Identification in Single-Cell Data

ITMO University

Saint-Petersburg, Russia

2022 - 2021

  • Thesis
  • Main goal of the project is to extend applications of the GAM-clustering tool on the single-cell RNA-seq data. In order to find optimal clustering algorithm performed and analysed multiple clustering strategies for the single-cell RNA-seq data. Used trajectories and gene set enrichment analysis for biological interpretation of the results. Involved in the modification of the tool.

Identifying Metabolic Modules in TCGA Datasets

ITMO University

Saint-Petersburg, Russia

2021

  • Course Project
  • With previousy developed GAM-clustering algorithm analyzed TCGA datasets (LUSC) - bulk RNA-seq data. Identified metabolic modules and performed biological analysis of them. During work was involved in the modification of the tool and testing.

Effects of Background RNA Noise on Differential Expression Results in scRNA-seq

ITMO University

Saint-Petersburg, Russia

2020

  • Performed standart analysis of the single-cell data with Seurat pipeline and integration of multiple samples using SCTransform intgration. With help of DropletUtils R package identified ambient RNA and tried to estimate the impact of it on the differential expression results.

Other Projects

vDiveR ShinyApp

Perdana University (Students Project)

N/A

Current - 2022

  • DiveR is a graphical user interface (GUI)-based web application hosted on R Shiny for the visualization of DiMA results, a tool designed to facilitate the dissection of protein sequence diversity dynamics for viruses.
  • Modifications of ShinyApp scripts
  • https://github.com/pendy05/vDiveR_RShiny

NGSprint Hackaton

NGSchool

Warsaw, Poland (online)

2021

  • Project: Data Visualization in Bioinformatics
  • Result: ShinyApp
  • Certificate by the link

Conferences

IMGC 2023

36th International Mammalian Genome Conference

Tsukuba, Japan (online)

2023

  • Evgeniia Chikina, Anastasiia Gainullina, Elena Shagimardanova, Alexander Nesmelov, Airat Bilyalov, Oleg Gusev, Roman Romanov. Hypothalamic cell diversity underlying behavioral differences in the American mink (Neogale vison).
  • The best virtual trainee poster

MCCMB’23

11th Moscow Conference on Computational Molecular Biology

Moscow, Russia

2023

  • Evgeniia Chikina, Victoria Melnikova, Anastasiia Gainullina, Roman A. Romanov. Hypothalamic neurons in type I diabetes at a single-cell resolution. ISBN 978-5-901158-33-3
  • Poster

Lomonosov 2023

30th International Scientific Conference for Undergraduate and Graduate Students and Young Scientists “Lomonosov”

Moscow, Russia

2023

  • Evgeniia Chikina. Study of diabetes-specific hypothalamic changes at the single cell level. ISBN 978-5-317-06952-0

Anniversary Scientific Conference «Nikolay Konstantinovich Koltzov and the Biology of the XXI century»

Koltzov Institute of Developmental Biology of Russian Academy of Sciences

Moscow, Russia

2022

  • Evgeniia Chikina, Anastasiia Gainullina, Roman A. Romanov. Metabolic modules of single cells of the hypothalamus in normal conditions and in metabolic disorders. ISBN 978-5-00204-554-9
  • Poster

Nationwide scientific forum of students and young scientists with international participation «Student science – 2018»

Saint-Petersburg State Pediatric Medical University

Saint-Petersburg, Russia

2018

Publications

iPSC-Derived Macrophages: The Differentiation Protocol Affects Cell Immune Characteristics and Differentiation Trajectories.

Klepikova, A.; Nenasheva, T.; Sheveleva, O.; Protasova, E.; Antonov, D.; Gainullina, A.; Chikina, E.; Sakovnich, O.; Gerasimova, T.; Nikitina, I.; et al. Int. J. Mol. Sci. 2022, 23, 16087. https://doi.org/10.3390/ijms232416087

N/A

2022

Achievements

IMGC 2023: Best virtual trainee poster

36th International Mammalian Genome Conference

Tsukuba, Japan (online)

2023

Bioinformatics Contest 2021

N/A

Stepik, Online

2021

Annual University Olympiad in Pediatrics

Saint-Petersburg State Pediatric Medical University

Saint-Petersburg, Russia

2018

  • 1st degree diploma

University Olympiad in Propaedeutics of Children’s Diseases

Saint-Petersburg State Pediatric Medical University

Saint-Petersburg, Russia

2017

  • 2nd degree diploma

Teaching experience

Chemistry/Biology School Tutor

N/A

Saint-Petersburg, Russia

2020 - 2018

  • I was teaching 6-9th grade school students chemistry and biology to increase their knowledge in the field and in some cases helped studying for school exams.

Courses

Introduction to Probability and Data with R (en)

Duke University

Coursera, Online

2022

Molecular biology of the cell (ru)

Bioinformatics Institute

Stepik, Online

2020

Programming in Python (ru)

Bioinformatics Institute

Stepik, Online

2019